Annotation

A note, added by way of comment, or explanation.

Composite Images

Layering of two or more images "on top" of each other with some amount of transparency applied to the foreground images.

Expression Detection

A process by which expressed cells are indicated for a given gene in a given tissue. This process can be automated or require expert annotation.

Gene

A hereditary determinant of a specific biological function, most often carried out by a specific protein encoded by the gene. In physical terms, a gene is a coding sequence of DNA that, when "expressed" through messenger RNA (mRNA) leads to the synthesis of a protein. Microarray studies (see below) are often referred to as "gene expression profiling."

Gene Expression Filter

An image that highlights those cells having the highest probability of gene expression above background labeling. Since the filter is presented as a single fixed image for each section, all displayed cells in the filter have exceeded an internally set threshold. At present, this threshold does not correspond to a specific probability or p-value of expression, but displays approximately 90% of all expressing cells.

Genome

The total set of genes carried by an individual or cell.

Hybridization

Reforming double-stranded DNA or RNA from complementary sequences. Synonym: annealing.

Image Registration

A software algorithm or process that deforms one image into another for the purpose of comparing common landmarks or regions.

in situ

in the natural or original position or place. Etymology: Latin, "in position."

In situ hybridization (ISH)

The hybridization of a DNA or RNA probe to complementary target sequences that are typically immobilized on microscope slide. In this context, the target sequences remain in a cell or a thin slice ("section") of tissue that may be derived from either normal or diseased tissue. The binding of a probe to a target is usually detected, following hybridization, by illuminating the specimen with a laser of specific wavelength that causes the probes to fluoresce. In the context of the Brain Atlas, the specimens or sections will be derived from various parts of the mouse brain.

ISH

see in situ hybridization (ISH).

Metadata

Data about data. Metadata describes how, when, and by whom a particular set of data was collected, and how the data is formatted and what type of data has been collected. Gender, strain, age, organism, and ISH catalogue date are all examples of metadata.

Neuroimaging

Computational mapping of the two-dimensional measurements from ISH onto a standard three-dimensional framework allowing for accurate three-dimensional reconstruction of the brain and visualization of the gene expression data.

Neuroconnections

Endogenous signaling molecules that alter the behavior of neurons or effector cells. Neurotransmitter is used here in its most general sense, including not only messengers that act directly to regulate ion channels, but also those that act through second messenger systems, and those that act at a distance from their site of release.

Neuropathways

A bundle of nerve fibers following a path through the brain.

Probe

A substance used to obtain specific information for diagnostic or experimental purposes. A probe is said to detect a "target." In genetic research, a probe is specifically a DNA or RNA fragment (usually labeled with a fluorescent chemical tag) that is designed to detect complementary DNA or RNA sequences by hybridization. In the context of in situ hybridization or microarrays (see below), a probe is DNA or RNA sequence usually 20 bases to 60 bases in length. Such short sequences are also called "oligonucleotides" or simply "oligos."

Target

A complementary DNA or RNA sequence detected by a probe. The usage of these terms is context-dependent. For in situ hybridization, the target is a DNA or RNA sequence in situ, i.e., in a cell or slice of tissue immobilized on a glass microscope slide, and the probe is a complementary, fluorescently-labeled DNA or RNA sequence in solution. In the context of microarray applications, the targets are fluorescently-labeled DNA or RNA sequences in solution and the probes are immobilized on a glass slide or silicon wafer.